MolNFT v1 · #169555 · protein
Class C beta-lactamase from escherichia COLI in complex with tazobactam
6XFS: “Class C beta-lactamase from escherichia COLI in complex with tazobactam”. X-ray diffraction, 1 ligand (TBE), 17 pockets (best druggability 0.70). MolNFT v1 #169555 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XFS
- Type
- protein
- Length
- 1,430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q104Z6
- Ligands
- TBE
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 38% helix, 23% strand | Q104Z6 |
| B, D | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 39% helix, 22% strand | Q104Z6 |
Ligands and binding sites
- TBE · Tazobactam intermediate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D
- PGE · Triethylene glycol · additive · 2 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.70 | 0.81 | 54 | PEG, TBE |
| 2 | 400 | 0.69 | 0.81 | 50 | TBE, EDO |
| 3 | 368 | 0.68 | 0.81 | 52 | TBE, PGE |
| 4 | 327 | 0.68 | 0.82 | 50 | TBE, EDO |
| 5 | 567 | 0.67 | 0.77 | 46 | empty |
Interfaces
4 interfaces between chains.
- B–C · 505 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 475 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 152 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6XFS · Class C beta-lactamase from Escherichia coli in complex with Tazobactam · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q104Z6
- Elsewhere: RCSB PDB 6XFS · PDBe 6XFS · UniProt Q104Z6
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